Variant report

Variant	rs9937139
Chromosome Location	chr16:74771367-74771368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74770638..74773504-chr16:74776084..74778878,2	MCF-7	breast:
2	chr16:74744325..74747304-chr16:74770344..74773194,2	MCF-7	breast:
3	chr16:74757597..74759698-chr16:74770601..74772220,2	MCF-7	breast:
4	chr16:74771230..74772064-chr5:171730704..171731663,2	Hela-S3	cervix:
5	chr16:74768107..74773823-chr16:74774706..74779558,7	K562	blood:
6	chr16:74763357..74765957-chr16:74768592..74772326,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103089	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1024503	1.00[ASN][1000 genomes]
rs10514386	1.00[ASN][1000 genomes]
rs11645307	0.83[GIH][hapmap];1.00[ASN][1000 genomes]
rs11864313	1.00[ASN][1000 genomes]
rs11864349	1.00[ASN][1000 genomes]
rs11866550	1.00[ASN][1000 genomes]
rs12444462	1.00[ASN][1000 genomes]
rs12444618	1.00[ASN][1000 genomes]
rs12445200	1.00[ASN][1000 genomes]
rs12446147	1.00[ASN][1000 genomes]
rs12447968	1.00[ASN][1000 genomes]
rs12919626	1.00[ASN][1000 genomes]
rs12921263	1.00[ASN][1000 genomes]
rs14308	1.00[ASN][1000 genomes]
rs2240251	0.87[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs241377	0.81[AFR][1000 genomes]
rs28810133	1.00[ASN][1000 genomes]
rs34130324	1.00[ASN][1000 genomes]
rs34393456	1.00[ASN][1000 genomes]
rs34398985	1.00[ASN][1000 genomes]
rs34937987	1.00[ASN][1000 genomes]
rs34992867	1.00[ASN][1000 genomes]
rs35038783	1.00[ASN][1000 genomes]
rs35173843	1.00[ASN][1000 genomes]
rs35195349	1.00[ASN][1000 genomes]
rs35456018	1.00[ASN][1000 genomes]
rs35937344	1.00[ASN][1000 genomes]
rs4887788	1.00[ASN][1000 genomes]
rs4888281	1.00[ASN][1000 genomes]
rs4888307	1.00[ASN][1000 genomes]
rs4985359	1.00[ASN][1000 genomes]
rs55836977	1.00[ASN][1000 genomes]
rs55859029	1.00[ASN][1000 genomes]
rs56009261	1.00[ASN][1000 genomes]
rs56313952	1.00[ASN][1000 genomes]
rs58303079	1.00[ASN][1000 genomes]
rs62052860	1.00[ASN][1000 genomes]
rs62052861	1.00[ASN][1000 genomes]
rs71392613	1.00[ASN][1000 genomes]
rs71392614	1.00[ASN][1000 genomes]
rs71392615	1.00[ASN][1000 genomes]
rs7203228	1.00[ASN][1000 genomes]
rs72794783	1.00[ASN][1000 genomes]
rs72796668	1.00[ASN][1000 genomes]
rs72796671	1.00[ASN][1000 genomes]
rs72796672	1.00[ASN][1000 genomes]
rs72796678	1.00[ASN][1000 genomes]
rs72796696	1.00[ASN][1000 genomes]
rs72798603	1.00[ASN][1000 genomes]
rs72798608	1.00[ASN][1000 genomes]
rs72798613	1.00[ASN][1000 genomes]
rs72798621	1.00[ASN][1000 genomes]
rs74024559	1.00[ASN][1000 genomes]
rs74024565	1.00[ASN][1000 genomes]
rs8047659	1.00[ASN][1000 genomes]
rs8062012	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv906907	chr16:74702254-74785902	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv517513	chr16:74743736-74812676	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
10	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
13	nsv457520	chr16:74758984-74907440	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv572976	chr16:74758984-74907440	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9937139	LDHD	cis	cerebellum	SCAN
rs9937139	MON1B	cis	parietal	SCAN
rs9937139	MON1B	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74762200-74772400	Enhancers	Fetal Thymus	thymus
2	chr16:74763200-74779000	Weak transcription	Right Atrium	heart
3	chr16:74764000-74781800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr16:74764400-74776000	Weak transcription	Spleen	Spleen
5	chr16:74764800-74771800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr16:74764800-74772200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr16:74764800-74774600	Weak transcription	Pancreas	Pancrea
8	chr16:74765000-74772600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr16:74765200-74774600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr16:74767800-74771600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:74768200-74773200	Enhancers	Brain Cingulate Gyrus	brain
12	chr16:74768400-74772000	Enhancers	Brain Substantia Nigra	brain
13	chr16:74768400-74772200	Enhancers	Brain Hippocampus Middle	brain
14	chr16:74768800-74774800	Weak transcription	HSMM	muscle
15	chr16:74769000-74771400	Weak transcription	NH-A	brain
16	chr16:74769000-74774800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr16:74769200-74771400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:74769200-74771400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr16:74769200-74772000	Weak transcription	Gastric	stomach
20	chr16:74769200-74772000	Weak transcription	HSMMtube	muscle
21	chr16:74769200-74777000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr16:74769200-74783200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr16:74769400-74772000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:74769400-74772200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:74769400-74776000	Weak transcription	Placenta	Placenta
26	chr16:74769400-74777400	Weak transcription	Fetal Lung	lung
27	chr16:74769400-74782800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr16:74769600-74775800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr16:74770000-74772200	Enhancers	Thymus	Thymus
30	chr16:74770200-74772400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:74770200-74772400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr16:74770200-74772800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr16:74770400-74772400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:74770400-74772400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr16:74770400-74772400	Enhancers	NHEK	skin
36	chr16:74770400-74772600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr16:74770400-74772800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr16:74770400-74772800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr16:74770400-74772800	Genic enhancers	Fetal Intestine Small	intestine
40	chr16:74770400-74773600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:74770400-74776000	Enhancers	Brain Angular Gyrus	brain
42	chr16:74770600-74771400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr16:74770600-74772000	Enhancers	A549	lung
44	chr16:74770600-74772800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr16:74770600-74772800	Enhancers	Esophagus	oesophagus
46	chr16:74770800-74772000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr16:74770800-74772200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr16:74770800-74772800	Enhancers	HMEC	breast
49	chr16:74770800-74773000	Enhancers	Stomach Mucosa	stomach
50	chr16:74771000-74771400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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